In the related art, a substrate processing apparatus is described in, for example, Japanese Patent Laid-Open Publication No. 11-087462. The substrate processing apparatus is a chemical mechanical polishing (CMP) apparatus that flatly polishes a surface of a substrate such as, for example, a silicon wafer. Such a substrate processing apparatus includes a substrate transfer section that transfers a substrate, a polishing section that polishes the substrate, and a cleaning section (cleaning apparatus) that cleans the substrate. The cleaning apparatus includes a cleaning module that removes fine particles such as, for example, residues of slurry used for CMP or metal polishing wastes. As the cleaning module, for example, a roll cleaning module using a roll cleaning member, a pencil cleaning module using a pencil cleaning member, and a two-fluid cleaning module using a two-fluid nozzle are known.